[phenixbb] real-space refinement hydrogens

Pavel Afonine pafonine at lbl.gov
Mon Jun 29 18:28:07 PDT 2020

Hi Alexei,

> When refining a crystal structure in phenix.refine, presence of 
> explicit hydrogens usually decreases the number of clashes.

that's a desirable outcome. But that depends on many factors and varies 
case by case.

> In the real-space refinement of a model against a cryo-EM map, 
> however, explicit hydrogens did not improve the clashscore. Is this 
> normal?

May be this is a case where they don't. And they may do in some other case.

> Does it depend on resolution?

Generally, yes. At higher resolution the map should have more impact.


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